ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPseqR")
AuthorPeter Humburg
Bioconductor views ChIPSeq Infrastructure
Date of publicationNone
MaintainerPeter Humburg <peter.humburg@gmail.com>
LicenseGPL (>= 2)
Version1.30.0

View on Bioconductor

Man pages

accessors: Access slots of S4 classes

alignFeature: Read counts relative to annotated features

BindScore: Class "BindScore"

callBindingSites: Predict protein binding sites from high-throughput sequencing...

ChIPseqR-package: Identifying Protein Binding Sites in High-Throughput...

compress-BindScore: Compress BindScore Objects

compress-methods: Methods for Function compress in Package 'ChIPseqR'

compress-ReadCounts: Compress ReadCount Objects

decompress: Extract Read Count and Binding Site Score Representations

decompress-methods: Methods for Function decompress in Package 'ChIPseqR'

exportBindSequence: Export sequence of predicted binding sites

getBindCor: Calculate cross-correlation between read counts

getBindLen: Estimate length of binding and support region

getCutoff: Determine significance threshold for binding site scores

internal: Internal and undocumented functions

pickPeak: Identify peaks above a given threshold

plot-BindScore: Diagnostic Plots for Binding Site Scores

plot-ReadCounts: Diagnostic Plots for Read Counts

plotReads: Plot compact representation of read counts on a chromosome

plotWindow: Plot read counts within a genomic region

pos2gff: Convert genome coordinates into GFF format

ReadCounts: Class "ReadCounts"

RLEBindScore-class: Run-length Encoded Binding Site Scores

RLEReadCounts-class: Run-length Encoded Read Counts

simpleNucCall: Predict nucleosome positions from high-throughput sequencing...

startScore: Score potential protein binding sites

strandPileup: Strand specific read counts

windowCounts: Summarize read counts in a sliding window

Functions

alignFeature Man page
allGroups Man page
allWords Man page
as.data.frame,BindScore-method Man page
binding Man page
binding,ANY-method Man page
binding,BindScore-method Man page
binding-methods Man page
BindScore Man page
[[,BindScore,ANY,missing-method Man page
[,BindScore,ANY,missing,missing-method Man page
[[,BindScore,ANY,numeric-method Man page
BindScore-class Man page
callBindingSites Man page
callBindingSites,ANY-method Man page
callBindingSites,character-method Man page
callBindingSites,matrix-method Man page
callBindingSites-methods Man page
callBindingSites,ReadCounts-method Man page
ChIPseqR Man page
ChIPseqR-package Man page
chrLength Man page
chrLength,BindScore-method Man page
chrLength,ReadCounts-method Man page
chrLength,RLEReadCounts-method Man page
compress Man page
compress-BindScore Man page
compress,BindScore-method Man page
compress-methods Man page
compress,ReadCounts-method Man page
compress,RLEBindScore-method Man page
compress,RLEReadCounts-method Man page
cutoff Man page
cutoff<- Man page
cutoff<-,ANY-method Man page
cutoff,ANY-method Man page
cutoff<-,BindScore-method Man page
cutoff,BindScore-method Man page
cutoff<--methods Man page
cutoff-methods Man page
decompress Man page
decompress,ANY-method Man page
decompress-methods Man page
decompress,RLEBindScore-method Man page
decompress,RleList-method Man page
decompress,Rle-method Man page
decompress,RLEReadCounts-method Man page
diNucTest Man page
exportBindSequence Man page
getBindCor Man page
getBindLen Man page
getCutoff Man page
head,BindScore-method Man page
lapply,BindScore-method Man page
lapply,ReadCounts-method Man page
length<-,BindScore-method Man page
length,BindScore-method Man page
length<-,ReadCounts-method Man page
length,ReadCounts-method Man page
max,BindScore-method Man page
min,BindScore-method Man page
names<-,BindScore,ANY-method Man page
names,BindScore-method Man page
names<-,ReadCounts,ANY-method Man page
names,ReadCounts-method Man page
nreads Man page
nreads,ReadCounts-method Man page
nreads,RLEReadCounts-method Man page
nullDist Man page
nullDist<- Man page
nullDist<-,ANY-method Man page
nullDist,ANY-method Man page
nullDist<-,BindScore-method Man page
nullDist,BindScore-method Man page
nullDist<--methods Man page
nullDist-methods Man page
oligoNucTest Man page
peaks Man page
peaks,ANY-method Man page
peaks,BindScore-method Man page
peaks-methods Man page
pickPeak Man page
plotBind Man page
plot,BindScore,missing-method Man page
plotFreq Man page
plot,ReadCounts,missing-method Man page
.plotReads Man page
plot,RLEReadCounts,missing-method Man page
.plotWindow Man page
pos2gff Man page
pvalue Man page
pvalue,ANY-method Man page
pvalue-methods Man page
range,BindScore-method Man page
ReadCounts Man page
$<-,ReadCounts,ANY-method Man page
[<-,ReadCounts,ANY,missing,ANY-method Man page
[[<-,ReadCounts,ANY,missing,ANY-method Man page
[<-,ReadCounts,ANY,missing-method Man page
[[<-,ReadCounts,ANY,missing-method Man page
[[,ReadCounts,ANY,missing-method Man page
[,ReadCounts,ANY,missing,missing-method Man page
ReadCounts-class Man page
$<-,ReadCounts-method Man page
$,ReadCounts-method Man page
RLEBindScore-class Man page
RLEReadCounts-class Man page
sapply,ReadCounts-method Man page
score Man page
score,BindScore-method Man page
simpleNucCall Man page
startScore Man page
strandPileup Man page
strandPileup,AlignedRead-method Man page
strandPileup,data.frame-method Man page
strandPileup-methods Man page
support Man page
support,ANY-method Man page
support,BindScore-method Man page
support-methods Man page
tail,BindScore-method Man page
triNucTest1 Man page
triNucTest2 Man page
views2nucFreq Man page
windowCounts Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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